Anatomical Identification at the Microscope using the Brain Navigation System

DESCRIPTION provided by applicant Microscopic analysis of histologic brain sections yields important information about the organization and composition of the nervous system particularly in modern studies focusing on neuro genomics transcriptomics proteomics and connectomics However identification of distinct brain regions in a section under study with the currently available tools printed or digital brain atlases is tedious and cumbersome and can even be misleading This Direct to Phase II project aims to develop a novel system for automatically identifying distinct brain regions in a section of a mouse brain being studied under a microscope by augmenting the section with graphical delineations and annotations of neuroanatomic regions in real time henceforth referred to as andquot brain navigation informationandquot the proposed Brain Navigation System tm BNS BNS will work as follows after placing a section of a mouse brain under a microscope the BNS software will i automatically generate a virtual slide of the section ii match the virtual slide image with the best fitting oblique angl slice through a digital D volume reconstruction of reference histology images from a reference mouse brain performed with the BNS Registration Match Finding and Identification Tool iii retrieve corresponding brain region delineations and annotations from a related digital D volume reconstruction of reference brain region delineations also performed with the BNS Registration Match Finding and Identification Tool and iv augment the section under study with brain navigation information either on the computer monitor or within the eyepieces of the microscope using our existing Lucivid r device performed with the BNS Visualization and Navigation Tool Brain navigation information will be retrieved from a special digital BNS Mouse Brain Atlas consisting of reference histology images and related reference brain region delineations that will be created with a special BNS Atlas Generation Tool A BNS Waxholm Bridge Tool will allow researchers to directly correlate their experimental specimens with a number of important reference tools on the internet such as the Allen Brain Connectivity Map etc The benefits of BNS for neuroscience research and society in general will be i objectivity validity reliability and substantial time savings for identifying brain regions inspcted under the microscope ii the potential for analyzing many more brain regions than is currently done thereby iii obtaining valuable additional information from brain sections that is currently not explored finally resulting in iv an improved basis for understanding how changes in neural activity contributes to mental disorders During pilot work performed in preparation for this project we proved feasibility of this novel andquot Registration Match Findingandquot technology by developing prototype software whose performance clearly exceeds the current state of the art in the field Work in Phase II will focus on i developing the production version of the different tools of BNS outlined above ii combining this technology with motorized microscope and XY specimen stage control and iii validating the full functionality of BNS PUBLIC HEALTH RELEVANCE Microscopic analysis of histologic brain sections yields important information about the organization and composition of the nervous system however identification of distinct brain regions in a section under study with the currently available tool printed or digital brain atlases is tedious and cumbersome and can even be misleading This project commercializes an innovative system for automatically identifying distinct brain regions in a section of a mouse brain being studied under a microscope and augmenting that section in real time with graphical delineations and annotations of neuroanatomic regions This system will not only help to reduce the currently intensely debated irreproducibility in basic research but wil enable researchers to analyze substantially more brain regions than is presently being done thereby obtaining additional valuable information from brain sections currently unexplored and resulting ultimately in an improved basis for developing novel treatment strategies for complex brain diseases